| posRMSDPot |
index |
potential terms restraining atomic positional RMSD.
restrains the position of selected atoms relative to those in other
members of an ensembleSimulation.EnsembleSimulation.
Constructor:
It is suggested that this potential term be created using the helper
functions posRMSDPotTools.create_BFactorPot() or
ncsPot.NCSPot().
PosRMSDPot(instanceName,
restraints="",
simulation) - creates a potential term with the given name.
restraints is an optional string of restraints.
simulation should specify the appropriate
EnsembleSimulation (default: currentSimulation)
Methods:
calcEnergy() - calcs energy
calcEnergyAndDerivs(DerivList) - calcs energy and derivative info
note that these routines also update all other potential-specific data.
addRestraints(restraints) - add restraints in the given string.
rms() - report rmsd value for this potential term.
numRestraints() - report number of restraints defined for this
term.
violations() - report number of violations for this term.
info() - return a string giving summary info for this
- term.
showRestraints(violated) - return a string listing restraints. If the
boolean violated is True, only violated
restraints are included, else all restraints are
listed.
showViolations() - return a string listing violated restraints.
showPositions() - return a string containing atom position info.
restraints() - return a list of restraints.
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.
Read-Write accessors:
scale - scale factor for potential
potType - potential type: 'harmonic' or 'square' [default: harmonic]
threshold - tolerance for violation determination.
centerSel - selection specifying qc. If it is empty, distances are
measured with respect to the origin.
rmsdType - string: either "bfactor" or "rap" [default: "bfactor"]
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 restraint class terms have the follow members
pot - the owning potential term.
calcd - the most recent calculated value.
obs - the observed value.
diff - for rmsdType='rap':
diff = calcd
for rmsdType='bfactor':
sqrt of V term.
see below.
obsErr - estimated error in obs
(obsErrB for rmsdType=='bfactor'
obsErrRAP for rmsdType=='rap' )
AtomSel sel - atomSel.AtomSel associated with the restraint.
avePos - list of average atomic positions in each ensemble member.
rmsd2_contrib - list of rsmd2 contributions from each ensemble member.
The potential term is defined as
E = scale() * V
where
for rmsdType='rap':
V = calcd
for rmsdType='bfactor':
V = Vsq(calcd-obs,obsErrB)
where,
q_{i,j} is the position of atom j in ensemble member i
qAve_j is the ensemble-averaged position of atom j
calcd = const sum_i w_i * rmsd2_contrib[i]
where
for rmsdType='rap':
const = 1
for rmsdType='bfactor':
const = 8*pi^2
rmsd2_contrib[i] = Vsq( | (q_ij-qc) - (qAve_j-qc) | , obsErrRAP)
and
Vsq(x,tol) = x^2 if potType=='harmonic'
(abs(x)-tol)^2 if potType=='square'
Restraints are entered in the format:
ASSIgn (atom selection) <obs> <err>
# 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 | ||
| ||