| prePot |
index |
PREPot Object - potential of restraints for PRE
reference:
J. Iwahara, C. Schwieters and G.M. Clore, JACS 126, 5879-5896 (2004).
(programed by Junji Iwahara)
Please use prePotTools.create_PREPot to create this potential term.
constructor: PREPot(instanceName,
restraintList,
dummy,
sel1Filter,
sel2Filter,
simulation)
instanceName : user-specified identifier
restraintList: optional XPLOR-style restraint table
dummy : optional unused legacy argument.
sel1Filter : set the sel1Filter member. See below for description.
sel2Filter : set the sel2Filter member. See below for description.
simulation : simulation.Simulation specification (optional)
Restraint Table Syntax:
-for normal-
ASSIgn (selection 1) (selection 2) Gobs error
-for nonstereo -
ASSIgn (selection 1) (selection 2) (selection 3) Gobs1 err1 Gobs2 err2
where Gobs is the PRE expressed in hertz. For nonstereo, the paramagnetic
center must be selection 1. The presence of selection 3 will toggle
the restraint's isStereoAssigned flag to False. This sort of restraint
is used for CH2 or NH2 protons that exhibit two resolved peaks but are not
stereospecifically assigned.
For either restraint type the numerical entries can be replaced by
the literal SUM:
ASSign (selection 1) (selection 2) SUM [weight]
then SUM-type restraints are indicated, with the Gobs and error
given by the subsequent ASSIgn statement. SUM restraints can also
take an optional weight after the SUM literal. The optional weight
can also be specified in the final entry, after the error value.
methods
addRestraints(restraintList) - add the specified XPLOR-style restraints
removeRestraint(num) - remove the specified restraint. Restraints
are numbered from zero. Note that
after a restraint is removed, all
restraints with larger indices will be
renumbered.
calcEnergy() - calc energy, returns the energy value.
calcEnergyAndDerivs(derivs) - calc energy, derivs, returns the energy value.
rms() - return the restraint violation
qFactor() - return Q-factor
rFactor() - return R-factor
correlation() - return correlation between calculated and observed PRE values.
violations() - return number of violations
simulation() - return the associated ensembleSimulation.EnsembleSimulation
showRestraints(violated) - return info on restraints. Argument violated is
boolean specifying whether to return only
violated restraints.
restraints() - return a sequence of restraints. See the description of the
Restraint class below.
ensWeight(index) - return the ensemble weight associated with the
specified member.
setEnsWeights(vals) - use the specified ensemble weights instead of those
in the underlying EnsembleSimulation.
mkSumRestraints(paraCenter,
weights) - convert restraints which have a selection which
matches paraCenter to SUM restraints- one for
each atom in a restraint selection which
matches paraCenter. The weights is an array
of weights to given these terms. If it is empty
weights of 1 are given.
The following parameters can be set [defaults in square brackets]
equType - Type of back-calculation of PRE
"sb" : the SB equation (SB mode) [default]
"sbmf" : the SBMF equation (SBMF mode)
aveType - Type of averaging
"r-6" : averaging with <r^(-6)>
"sum" : sum over r^(-6) terms, dividing by aveSize, or:
1/aveSize \sum r^{-6}
aveSize - used only for aveType=="sum". See previous entry.
rlxType - Type of paramagnetic relaxation mechanism
"r2dd" : R2 relaxation enhancement by dipolar mechanism
"r2curie" : by Curie spin relaxation
"r2mix" : r2dd + r2curie
"r1dd" : R1 relaxation enhancement by dipolar mechanism
"r1curie" : by Curie spin relaxation
"r1mix" : r1dd + r1curie
For the SBMF mode, only r2dd and r1dd are supported.
funType - Type of penalty function
"correlation" : optimize correlation between calculated and
observed values
"square" : Squared well potential
"harmonic" : Harmonic potential [default]
"onesixth" : ((Gcal)^(-1/6)-(Gobs)^(-1/6))^2
potType - Energy form for large violations
"hard" : quadratic penalty for large errors [default]
"soft" : switchover to linear penalty function for large errors
For potType="soft", the asympotic energy function becomes:
ret *= A + B / pow(r,softExp) + asympSlope * r;
where r = calcd - obs PRE value, and A and B are determined
such that the energy and its first derivative are continuous at
r = rSwitch.
sclType - Type of scaling
"const" : Constant scaling.
1.0 for all
"sigma" : Scaling based on error.
1.0/(error)^2
"obsig" : Scaling based on Gobs and error
Gobs/Gmax/(error)^2
sbmfType - Which correlation time to specify
"taut" : specify taut [default]
"taui" : specify taui
The time which is not specified is computed via the equation:
1/tau_t = 1/tau_c + 1/tau_i
sel1Filter - used to filter the restraints specified in input restraint
specifications. The first set of atoms used become the
intersection of those specified in the restraint and sel1Filter.
The setting of this member only affects restraints read after
applying the setting.
sel2Filter - same for the second (and third, if specified) set of atoms.
fixTauc - whether tau_c is fixed (True) or optimized (False) [True].
If False, clock atoms must be set with setTaucAtoms().
tcMin - bounds for tauc, when TcType "opt" is specified.
tcMax
fixTaut - whether tau_t is fixed (True) or optimized (False) [True]
If False, clock atoms must be set with setTautAtoms().
fixTaui - whether tau_i is fixed (True) or optimized (False) [True]
If False, clock atoms must be set with setTauiAtoms().
tiMin - bounds for taui when TiType "opt" is specified.
tiMax
ensInterconvert - how to treat averaging over EnsembleSimulation members-
for SBMF mode. [Default: fast]
"fast" : include average over EnsembleSimulation members in
calculation of order parameters and distance ave.
"slow" : for each EnsembleSimulation member, calculate the
averages over ensemble of tags, and then perform
a linear EnsembleSimulation-weighted sum to compute
Gamma.
rSwitch - for soft potType, value of calcd-obs PRE for which to switch
over to the asymptotic form of the energy function.
softExp - exponent for asymptotic form of the energy function.
asympSlope - slope for asymptotic form of the energy function.
verbose - if true, sporadically spit out info [False]
threshold - threshold in violation calculation [0.1]
showAllRestraints - boolean which changes the behavior of showViolations. If
this parameter is set to True, the behavior of
showViolations is modified such that all restraints are
printed. Violated restraints are indicated by an
asterisk in the first column. [1]
useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
or to use those of the underlying EnsembleSimulation.
npc - number of paramagnetic centers [1]
(This is NOT the number of tag conformers)
For instance, ncp=2 for a homodimer in which the individual
subunits each have a single paramagentic center. This is,
rather, a multiplicative prefactor in the calculation of the
1/r^6 sum to account for summing due to the presence of
multiple paramagnetic centers, or equivalent nuclei undergoing
paramagnetic relaxation.
rho0 - constant prefactor used for scaling PRE values when tauc is not
fit [1].
expTemp - temperature (only for r2curie, r2mix, r1curie, r1mix) [300]
taur - rotational correlation time
(only for r2curie, r2mix, r1curie, r1mix)
tauc - correlation time (1/tc = 1/tr + 1/ts)
taut - overall correlation time in the SBMF equation (1/tt=1/tc+1/ti)
freqI - NMR frequency (MHz) [500.0]
gfac - electron g-factor [2.0]
sqn - electron spin quantum number [2.5]
gammaI - nuclear gyromagnetic ratio [26.752196]
useDistMultMat - boolean specifying whether to use distMultMat [False].
distMultMat - a row-major matrix (or 2D list) of dimension len(sel1)x
len(sel2) specifying multipiers of the i,j 1/r^6 distance
contributions to the PRE.
Unit of correlation times are nano-seconds.
the above quantities may be retrieved using the member function form
quantity(), while they are set using the form setQuantity(value).
Restraint class
members/methods:
name() - the restraint name
comment() - the restraint comment (entered after the ! in the PRE table)
sel1 - an atomSel.AtomSel corresponding to the first selection
in the restraint table.
sel2 - an atomSel.AtomSel corresponding to the second selection
in the restraint table.
sel3 - an atomSel.AtomSel corresponding to the second selection
in the restraint table.
asString() - a string representation of the restraint.
gamma() - return calculated Gamma
g() - observed PRE (Gamma)
gSigma() - error in observed PRE (Gamma)
weight() - weight on this restraint - depends on sclType()
sumTerms() - for non-sum terms: 0
for sum terms: -1 for all but last: the number of sum terms.
sumWeight()- weight of contribution of this sum term.
contrib() - return Gamma contribution from this SUM term
status() - return LESS, INSIDE or GREATER for position in square well.
isStereoAssigned() - whether a third selection is present in the assignment
statement. See above.
vectors
i6contrib;
sri6_contrib;
s2ang_contrib;
s2rad_contrib;
sri6_contribB;
s2ang_contribB;
s2rad_contribB;
float numbers
s2angular()
s2radial()
reff();
for NONSTEREO
vector:
i6contribB
floats
contribB()
gammaB()
gB()
gBSigma()
reffB()
s2angularB()
s2radialB()
s2B()
sumCalc()
sumObs()
difCalc()
difObs()
smallObs()
largeObs()
smallCalc()
largeCalc()
emstatus() - returns EM1 EM2 or EM3 in analogy to status()
# 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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