| sardcPot |
index |
sardcPot
steric alignment residual dipolar coupling potential
See: Jie-rong Huang, Stephan Grzesiek,``Ensemble calculations of
unstructured proteins constrained by RDC and PRE data: a case study of
urea-denatured ubiquitin'', J. Am. Chem. Soc. 132, 694-705 (2010).
constructor:
SARDCPot(instanceName, tensor, restraints)
-instanceName is a user-specified identifier.
-tensor is a saTensor.SATensor object which describes the
steric aligment tensor.
-restraints is an restraint table (the format is described below)
methods:
linkTo(term) - specify an SARDC potential term with which
to share avectorScale. In a PotList,
the term specified in linkTo should be
before the current term.
irredTensor(member) - given a ensemble member index, return
the scaled alignment tensor in irreducible
form. If member index is omitted, that of
the current ensemble member is returned.
chisq() - Obtain the chi-squared value
addRestraints(string,
useDist=False,
useSign=True )- add restraints. The 1/r^3 distance dependence
of each restraint can be enabled by specifying
useDist=True, while the sign can be ignored
with useSign=False.
calcEnergy() - calc energy, returns the energy value.
calcEnergyAndDerivs(derivs) - calc energy, derivs, returns
the energy value.
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.
The following members can be read using the method named member() and set
using the method setMember(val) [defaults in square brackets]
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", "average", or "pairwise". In pairwise
averaging, the two atom selections for each
restraint must selection the same number of atoms,
and the averaging is done in order over pairs of
atoms from each selection. This is useful for
multimers whose subunits are labeled with
different segids. ["average"]
avectorScale - the overall scale factor (determined from
fit to experiment) applied to the alignment
tensor.
optimizeScale - boolean which, if False, disables the automatic
optimization of avectorScale. [True]
omitTensorGrad - boolean which, if True, disables computation of
the gradient with respect to the alignment
tensor. This can be useful in late stages of
refinement to prevent unphysical distortions of
surface regions. [False]
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. [False]
public members:
tensor - the associated saTensor.SATensor used for
alignment.
avectorScaleUp - numerator in computation of avectorScalea
avectorScaleDown - denominator in computation of avectorScalea
assignment table:
entries in the restraint list can have the following form
assign ( sel m ) ( sel n ) obs error1 error2 distance useSign
where the m and n selections specify the atoms involved in the interaction.
The observed RDCs are given by obs argument.
The error bounds are given by error1 and error2. If error2 is set
as 0, it defaults to error1. The argument of distance can be
defined for fixed geometry RDCs. For variable distances, this
argument is set to 0. If the sign of observed RDCs is sure, set as
0; otherwise set as 1. See the above entry for aveType for the
handling of selections containing multiple atoms. Alternatively, the
restraints can be in the format specified in rdcPot.
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
aSelection() - atomSel for atom A
bSelection() - atomSel for atom B
calced_contrib() - list of contributions due to each ensemble member.
deviation() - measure of spread between different ensemble members
Dmax() - the value of the dipolar coupling prefactor, known internally
as scale. This includes the product of gyromagnetic ratios,
divided by r^3, if useDistance=False.
The following members can be read using member() or set using setMember().
I.e. restraint.setObs( 1.2 )
obs - observed RDC value
useSign - whether to use the sign of the RDC
useDistance - If true, divide the computed RDC by r_AB^3, where r_AB is the
distance between nuclei in the structure.
err - the experimental error.
# 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.
| Classes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Functions | ||
| ||