| rdcPot | index rdcPot.py |
residual dipolar coupling potential
One normally creates RDCPot objects using the create_RDCPot function within
the rdcPotTools module.
constructor:
RDCPot1(instanceName,
oTensor
restraints,
simulation)
instanceName is a user-specified identifier. oTensor specifies an
orientational varTensor.VarTensor object. restraints is an optional
XPLOR-style sani or dipo restraint table. simulation is an optional
simulation.Simulation specification.
This potential term is described in G.M. Clore and C.D. Schwieters,
J. Am. Chem. Soc. 126, 2923-2938 (2004).
members:
oTensor - the VarTensor orientational tensor object.
methods:
addRestraints(restraintList) - add the specified XPLOR sani- or
dipo-style restraints. Note that this is a
string, and not a filename.
calcEnergy() - calc energy, returns the energy value.
calcEnergyAndDerivs(derivs) - calc energy, derivs, returns the energy value.
rms() - return the rms of calcedShift - effShift
deviation() - return average of deviation of ensemble members
numRestraints() - return the number of restraints defined for this term.
violations() - return number of violations
info() - current info about the state of this instance
showViolations() - return a string listing violated restraints.
showRestraints(violated) - return info on restraints. Argument violated is
boolean specifying whether to return only
violated restraints.
restraints() - return a list of restraints. See the description of the
Restraint class below.
rawRestraints() - return a list of restraints, without calling calcEnergy
to update calculated values. See the description of the
Restraint class below.
simulation() - return the associated simulation.Simulation.
ensWeigth(index) - return the ensemble weight associated with the
specified member.
setEnsWeights(vals) - use the specified ensemble weights instead of those
in the underlying EnsembleSimulation.
The following parameters can be set [defaults in square brackets]
deltaDFS - constant offset in dipolar couplings [0]
verbose - if true, sporadically spit out info [False]
useDistance- if true, include the 1/r^3 dependence in the calcedShift
calculation. Note that this feature changes the meaning
and units of Da [0].
useSign - default value for useSign of each restraint (see restraint
description below) [True]. When set with setUseSign(), the
default value, and values of all restraints are set.
gyroA
gyroB - linear scaling factors for the calculated dipolar coupling.
scale - scale factor (force constant) [1]
threshold - threshold in violation calculation [0]
potType - type of potential: "harmonic" or "square" ["harmonic"]
aveType - type of averaging to use for indistinguishable atoms:
"sum" or "average" ["average"]
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. [0]
useSimEnsWeight - whether to use the ensemble wieghts set with setEnsWeights
or to use those of the underlying EnsembleSimulation.
the above quantities may be retrieved using the member function form
quantity(), while they are set using the form setQuantity(value).
assignment table:
entries in the restraint list have the following form
assign ( sel OO ) ( sel Z ) ( sel X ) ( sel Y )
( sel m ) ( sel n ) obsShift error1 [error2]
[or ( sel m1 ) ( sel n1) ...]
where the first four selections are present for compatibility with
XPLOR assignment tables. the m and n selections specify the atoms
involved in the interaction. The observed dipolar shift is given by
the obsShift argument, and the error bounds are given by error1 and
error2. If error2 is absent, it defaults to error1. One or more
optional OR statements can be used to add additional pairs of atom
selections. For instance, is residue 4 is a phenylalanine, the
following assign..or statement will correctly allow averaging of the
CE1-HE1 CE2-HE2 contributions:
assign ( resid 500 and name OO )
( resid 500 and name Z )
( resid 500 and name X )
( resid 500 and name Y )
( resid 4 and name CE1 )
( resid 4 and name HE1 ) -4.62 4.62 0.1000
or ( resid 4 and name CE2 )
( resid 4 and name HE2 )
[ If a single pair of wildcard atom selections is used, four
contributions are computed. For these cases, the RDCPot assignment
statement is not compatible with XPLOR DIPO ASSIgnment
statements. ]
The dipolar shift is given by the equation
calcedShift = DFS + Da (3 vz^2 -1) + 3/2 Da*R ( vx^2 - vy^2 )
where R is the rhombic tensor component, and vx,vy,vz are the
projections of the unit vector in the direction mn onto the
corresponding coordinate axis representing tensor orientation. Da is scaled
by gyroA and gyroB. Typically, these are set to one, or are set to scale
factors such that a single Da value can be used with experiments
involving different nuclei. These scale factors are usually set
using the helper function rdcPotTools.scale_toNH.
If useDistance is 1, the Da is scaled by 1 / |q_m - q_n|^3. Note that
this changes the units of Da. This feature is frequently used in
proton-proton experiments. If the Da is fixed, one will need an
additional experiment to obtain a value for Da, and the value scaled
appropriately. For example, if Da(NH) is available from a 15N-1H
experiment in the same medium, the H-H Da would be set as Da(NH) *
r(NH)^3 * gamma(N) gamma(N) = 10.47*Da(NH), where r(NH) is the NH
bond distance, and gamma(N) and gamma(H) are the gyromagnetic ratio
of 15N and 1H, respectively.
The energy function is defined as
1/2 * scale * (calcedShift - effShift)^2 [for useSign==True]
or
1/2 * scale * (|calcedShift| - |effShift|)^2 [for useSign==False]
where for potType=harmonic, effShift = obsShift. For potType=square,
effShift = calcedShift, if
obsShift-error1 < calcedShift < obsShift+error2
= calcedShift+error1, if calcedShift < obsShift-error1
= calcedShift-error2, if calcedShift > obsShift+error2
Restraint class
methods:
energy() - energy due to this restraint
calcd() - calculated value of dipolar coupling (ensemble average).
obs() - observed value of dipolar coupling.
diff() - difference between calcd and obs
plusErr(), minusErr() - bounds for the square well potential
selPairs() - pairs of atom selections. Each pair is an object with
atomSel.AtomSel members named a and b,
corresponding to the first and second selections in the
ASSIgn or OR statements
aSelection() - deprecated - synonym for selPairs()[0].a
bSelection() - deprecated - synonym for selPairs()[0].b
calced_contrib() - list of contributions due to each ensemble member.
deviation() - measure of spread between different ensemble members
useSign() - if false, ignore the sign of the calculated and observed
dipolar coupling; this if the sign of the shift is
unknown [True]. Set this using the setUseSign accessor.
# This file was created automatically by SWIG.
# Don't modify this file, modify the SWIG interface instead.
# This file is compatible with both classic and new-style classes.
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| __package__ = None pyXplorHelp = Type help() for interactive help, or help(object) for help about object. | ||